Last updated: 2019-02-19
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Ignored files:
Ignored: analysis/figure/
Ignored: code/.ipynb_checkpoints/
Ignored: data/
Ignored: output/10x-180504
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Ignored: output/monocle/
Untracked files:
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Untracked: analysis/10x-180831-analysis.Rmd
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Deleted: analysis/.ipynb_checkpoints/velocyto_notebook_180504-checkpoint.ipynb
Modified: analysis/10x-180504-general-analysis.Rmd
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#library(workflowr, lib.loc='/home/cbmr/pytrik/libraries/')
#library(Seurat, lib.loc='/home/cbmr/pytrik/libraries/')
seurobj <- readRDS('output/10x-180831')
PC2 seems to capture the difference between Monocle states.
DimPlot(seurobj, group.by='State', reduction.use='pca', dim.1=5, dim.2=2)
How are some of the branch-dependent genes expressed? Brown genes
FeaturePlot(seurobj, features.plot=c('UCP2', 'FABP5', 'GPD1', 'ADIPOQ'), reduction.use='pca', dim.1=5, dim.2=2, cols.use=c('gray', 'blue'), no.legend=F, nCol=2)
White genes
FeaturePlot(seurobj, features.plot=c('APOD', 'MGP', 'IGF2', 'PLAC9'), reduction.use='pca', dim.1=5, dim.2=2, cols.use=c('gray', 'blue'), no.legend=F, nCol=2)
Expression of brown branch genes in the t-SNE
FeaturePlot(seurobj, features.plot=c('UCP2', 'FABP5', 'SCD', 'G0S2', 'ADIPOQ', 'GPD1', 'PLIN1', 'PLIN4'), reduction.use='tsne', cols.use=c('gray', 'blue'), no.legend=F, nCol=2)
Some of the white branch genes
FeaturePlot(seurobj, features.plot=c('APOD', 'MGP', 'DCN', 'PLAC9', 'IGF2', 'ZFP36', 'FOS',
'TCEAL4',
'C1R',
'OSR2',
'MFGE8',
'FBLN1',
'CLU'), reduction.use='tsne', cols.use=c('gray', 'blue'), no.legend=F, nCol=2)
PC2 heatmap
PCHeatmap(seurobj, pc.use=2, cells.use=100, do.balanced = T, num.genes = 100)
Warning in heatmap.2(data.use, Rowv = NA, Colv = NA, trace = "none", col = col.use, :
Discrepancy: Rowv is FALSE, while dendrogram is `both'. Omitting row dendogram.
Warning in heatmap.2(data.use, Rowv = NA, Colv = NA, trace = "none", col = col.use, :
Discrepancy: Colv is FALSE, while dendrogram is `column'. Omitting column dendogram.
Warning in plot.window(...): "dimTitle" is not a graphical parameter
Warning in plot.xy(xy, type, ...): "dimTitle" is not a graphical parameter
Warning in title(...): "dimTitle" is not a graphical parameter
FeaturePlot(seurobj, features.plot=c('ADIPOQ', 'LIPE', 'PLIN4', 'FASN', 'AGPAT2', 'PCK1', 'MMP2', 'PPAP2B', 'SCARA5', 'IGFBP6', 'SERPING1'), reduction.use='tsne', cols.use=c('gray', 'blue'), no.legend=F, nCol=2)
FeaturePlot(seurobj, features.plot='EBF2', cols.use=c('gray', 'blue'), no.legend=F)
sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Storage
Matrix products: default
BLAS: /nfsdata/tools/R/3.4.3/lib64/R/lib/libRblas.so
LAPACK: /nfsdata/tools/R/3.4.3/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Seurat_2.3.4 Matrix_1.2-15 cowplot_0.9.4 ggplot2_3.1.0 workflowr_1.1.1
loaded via a namespace (and not attached):
[1] Rtsne_0.13 colorspace_1.4-0 class_7.3-14 modeltools_0.2-22
[5] ggridges_0.5.0 mclust_5.4.1 rprojroot_1.3-2 htmlTable_1.12
[9] base64enc_0.1-3 rstudioapi_0.9.0 proxy_0.4-22 flexmix_2.3-14
[13] bit64_0.9-7 mvtnorm_1.0-8 codetools_0.2-16 splines_3.4.3
[17] R.methodsS3_1.7.1 robustbase_0.93-2 knitr_1.20 jsonlite_1.6
[21] Formula_1.2-3 ica_1.0-2 cluster_2.0.7-1 kernlab_0.9-27
[25] png_0.1-7 R.oo_1.22.0 compiler_3.4.3 httr_1.3.1
[29] backports_1.1.2 assertthat_0.2.0 lazyeval_0.2.1 lars_1.2
[33] acepack_1.4.1 htmltools_0.3.6 tools_3.4.3 bindrcpp_0.2.2
[37] igraph_1.2.2 gtable_0.2.0 glue_1.3.0 RANN_2.6
[41] reshape2_1.4.3 dplyr_0.7.6 Rcpp_0.12.18 trimcluster_0.1-2.1
[45] gdata_2.18.0 ape_5.1 nlme_3.1-137 iterators_1.0.10
[49] fpc_2.1-11.1 gbRd_0.4-11 lmtest_0.9-36 stringr_1.3.1
[53] irlba_2.3.2 gtools_3.8.1 DEoptimR_1.0-8 MASS_7.3-50
[57] zoo_1.8-3 scales_1.0.0 doSNOW_1.0.16 parallel_3.4.3
[61] RColorBrewer_1.1-2 yaml_2.2.0 reticulate_1.10 pbapply_1.3-4
[65] gridExtra_2.3 rpart_4.1-13 segmented_0.5-3.0 latticeExtra_0.6-28
[69] stringi_1.2.4 foreach_1.4.4 checkmate_1.8.5 caTools_1.17.1.1
[73] bibtex_0.4.2 Rdpack_0.9-0 SDMTools_1.1-221 rlang_0.3.1
[77] pkgconfig_2.0.2 dtw_1.20-1 prabclus_2.2-6 bitops_1.0-6
[81] evaluate_0.11 lattice_0.20-38 ROCR_1.0-7 purrr_0.2.5
[85] bindr_0.1.1 labeling_0.3 htmlwidgets_1.2 bit_1.1-14
[89] tidyselect_0.2.4 plyr_1.8.4 magrittr_1.5 R6_2.4.0
[93] snow_0.4-2 gplots_3.0.1 Hmisc_4.1-1 whisker_0.3-2
[97] pillar_1.3.1 foreign_0.8-71 withr_2.1.2 fitdistrplus_1.0-9
[101] mixtools_1.1.0 survival_2.42-6 nnet_7.3-12 tsne_0.1-3
[105] tibble_2.0.1 crayon_1.3.4 hdf5r_1.0.0 KernSmooth_2.23-15
[109] rmarkdown_1.10 grid_3.4.3 data.table_1.11.4 git2r_0.24.0
[113] metap_1.0 digest_0.6.16 diptest_0.75-7 tidyr_0.8.1
[117] R.utils_2.7.0 stats4_3.4.3 munsell_0.5.0
This reproducible R Markdown analysis was created with workflowr 1.1.1